annotate macros.xml @ 22:9a913cdee30e draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
author iuc
date Wed, 03 Nov 2021 15:17:39 +0000
parents
children abfd8a6544d7
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
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1 <macros>
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
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2 <token name="@TOOL_VERSION@">1.11</token>
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
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3 <token name="@VERSION_SUFFIX@">0</token>
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
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4 <xml name="bio_tools">
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
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5 <xrefs>
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
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6 <xref type="bio.tools">multiqc</xref>
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
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7 </xrefs>
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
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8 </xml>
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
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9 <xml name="requirements">
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
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10 <requirements>
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
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11 <requirement type="package" version="@TOOL_VERSION@">multiqc</requirement>
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
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12 </requirements>
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
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13 </xml>
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
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14
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
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15 <token name="@ESCAPE_IDENTIFIER@">
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
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16 <![CDATA[
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
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17 #set identifier = re.sub('[^\s\w\-]', '_', str($file.element_identifier))
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
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18 ]]></token>
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
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19
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
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20 <token name="@CHECK_LN_FILE@">
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
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21 <![CDATA[
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
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22 #if $file_path in $file_paths
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
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23 #set $file_path += '_' + str($file_paths.count($file_path))
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
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24 #end if
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
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25 #set $file_paths += [$file_path]
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
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26 grep -q '$pattern' $file || die "Module '${repeat.software_cond.software}: '$pattern' not found in the file '$identifier'" &&
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
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27 ln -s '$file' '$file_path' &&
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
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28 ]]></token>
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
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29
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
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30 <token name="@CREATE_REPEAT_DIR_1@">
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
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31 <![CDATA[
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
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32 #set repeat_dir = os.path.join($software_dir, str($repeat2.type) + '_' + str($j))
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
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33 mkdir '$repeat_dir' &&
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
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34 ]]></token>
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
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35
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
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36 <token name="@CREATE_REPEAT_DIR_1@">
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
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37 <![CDATA[
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
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38 #set repeat_dir = os.path.join($software_dir, str($repeat2.type) + '_' + str($j))
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
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39 mkdir '$repeat_dir' &&
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
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40 ]]></token>
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
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41 <token name="@CREATE_REPEAT_DIR_2@">
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
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42 <![CDATA[
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
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43 #set repeat_dir = os.path.join($software_dir, str($repeat2.type.type) + '_' + str($j))
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
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44 mkdir '$repeat_dir' &&
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
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45 ]]></token>
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
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46 <token name="@LN_FILES@">
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
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47 <![CDATA[
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
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48 #set file_paths = []
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
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49 #for $file in $repeat.software_cond.input
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
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50 @ESCAPE_IDENTIFIER@
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
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51 #set file_path = os.path.join($software_dir, str($identifier))
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
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52 @CHECK_LN_FILE@
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
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53 #end for
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
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54 ]]></token>
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
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55
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
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56 <token name="@LN_2_FILES@">
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
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57 <![CDATA[
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
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58 #set file_paths = []
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
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59 @CREATE_REPEAT_DIR_1@
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
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60 #for $file in $repeat2.input
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
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61 #set identifier = re.sub('[^\s\w\-]', '_', str($file.element_identifier))
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
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62 #set file_path = os.path.join($repeat_dir, str($identifier))
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
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63 @CHECK_LN_FILE@
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
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64 #end for
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
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65 ]]></token>
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
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66
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
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67 <token name="@LN_3_FILES@">
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
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68 <![CDATA[
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
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69 #set file_paths = []
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
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70 #for $file in $repeat2.type.input
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
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71 #set identifier = re.sub('[^\s\w\-]', '_', str($file.element_identifier))
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
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72 #set file_path = os.path.join($repeat_dir, str($identifier))
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
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73 @CHECK_LN_FILE@
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
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74 #end for
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
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75 ]]></token>
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
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76
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
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77 <token name="@BISMARK_INPUT@"><![CDATA[
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
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78 #for $j, $repeat2 in enumerate( $repeat.software_cond.output )
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
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79 @CREATE_REPEAT_DIR_1@
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
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80 #if str($repeat2.type) == "align"
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
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81 #for $file in $repeat2.input
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
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82 @ESCAPE_IDENTIFIER@
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
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83 #set file_path = os.path.join($repeat_dir, str($identifier) + '_SE_report.txt')
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
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84 ln -s '$file' '$file_path' &&
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
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85 #end for
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
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86 #elif str($repeat2.type) == "dedup"
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
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87 #for $file in $repeat2.input
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
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diff changeset
88 @ESCAPE_IDENTIFIER@
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
89 #set file_path = os.path.join($repeat_dir, str($identifier) + '_deduplication_report.txt')
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
90 ln -s '$file' '$file_path' &&
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
91 #end for
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
92 #elif str($repeat2.type) == "meth_extract"
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
93 #for $file in $repeat2.input
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
94 @ESCAPE_IDENTIFIER@
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
95 #set file_path = os.path.join($repeat_dir, str($identifier) + '_splitting_report.txt')
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
96 ln -s '$file' '$file_path' &&
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
97 #end for
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
98 #elif str($repeat2.type) == "m_bias"
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
99 #for $file in $repeat2.input
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
100 @ESCAPE_IDENTIFIER@
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
101 #set file_path = os.path.join($repeat_dir, str($identifier) + '_M-bias.txt')
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
102 ln -s '$file' '$file_path' &&
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
103 #end for
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
104 #elif str($repeat2.type) == "bam2nuc"
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
105 #for $file in $repeat2.input
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
106 @ESCAPE_IDENTIFIER@
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
107 #set file_path = os.path.join($repeat_dir, str($identifier) + '.nucleotide_stats.txt')
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
108 ln -s '$file' '$file_path' &&
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
109 #end for
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
110 #end if
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
111 #end for
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
112 ]]></token>
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
113
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
114 <token name="@DEEPTOOLS_INPUT@"><![CDATA[
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
115 #for $j, $repeat2 in enumerate( $repeat.software_cond.output )
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
116 #if str($repeat2.type) == "bamPEFragmentSize"
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
117 #set $pattern = "Frag."
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
118 @LN_2_FILES@
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
119 #elif str($repeat2.type) == "estimateReadFiltering"
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
120 #set $pattern = "Internally-determined Duplicate"
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
121 @LN_2_FILES@
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
122 #elif str($repeat2.type) == "plotCoverageStdout"
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
123 #set $pattern = "sample"
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
124 @LN_2_FILES@
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
125 #elif str($repeat2.type) == "plotCoverageOutRawCounts"
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
126 #set $pattern = "#plotCoverage --outRawCounts"
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
127 @LN_2_FILES@
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
128 #elif str($repeat2.type) == "plotEnrichment"
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
129 #set $pattern = "featureReadCount"
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
130 @LN_2_FILES@
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
131 #elif str($repeat2.type) == "plotFingerprintOutRawCounts"
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
132 #set $pattern = "#plotFingerprint --outRawCounts"
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
133 @LN_2_FILES@
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
134 #end if
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
135 #end for
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
136 ]]></token>
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
137
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
138 <token name="@PICCARD_INPUT@"><![CDATA[
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
139 #for $j, $repeat2 in enumerate( $repeat.software_cond.output )
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
140 #if str($repeat2.type) == "alignment_metrics"
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
141 #set $pattern = "picard.analysis.AlignmentSummaryMetrics"
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
142 @LN_2_FILES@
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
143 #elif str($repeat2.type) == "basedistributionbycycle"
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
144 #set $pattern = "picard.analysis.BaseDistributionByCycleMetrics"
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
145 @LN_2_FILES@
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
146 #elif str($repeat2.type) == "gcbias"
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
147 #set $pattern = "picard.analysis.GcBias"
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
148 @LN_2_FILES@
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
149 #elif str($repeat2.type) == "hsmetrics"
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
150 #set $pattern = "picard.analysis.directed.HsMetrics"
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
151 @ @
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
152 #elif str($repeat2.type) == "insertsize"
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
153 #set $pattern = "picard.analysis.InsertSizeMetrics"
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
154 @LN_2_FILES@
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
155 #elif str($repeat2.type) == "markdups"
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
156 #set $pattern = "MarkDuplicates"
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
157 @LN_2_FILES@
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
158 #elif str($repeat2.type) == "oxogmetrics"
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
159 #set $pattern = "picard.analysis.CollectOxoGMetrics"
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
160 @LN_2_FILES@
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
161 #elif str($repeat2.type) == "pcr_metrics"
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
162 #set $pattern = "picard.analysis.directed.TargetedPcrMetrics"
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
163 @LN_2_FILES@
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
164 #elif str($repeat2.type) == "rnaseqmetrics"
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
165 #set $pattern = "Collect"
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
166 @LN_2_FILES@
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
167 #elif str($repeat2.type) == "rrbs_metrics"
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
168 #set $pattern = "picard.analysis.RrbsSummaryMetrics"
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
169 @LN_2_FILES@
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
170 #elif str($repeat2.type) == "wgs_metrics"
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
171 #set $pattern = "picard.analysis.CollectWgsMetrics$WgsMetrics"
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
172 @LN_2_FILES@
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
173 #end if
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
174 #end for
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
175 ]]></token>
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
176
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
177 <token name="@FASTQC_INPUT@"><![CDATA[
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
178 #for $j, $repeat2 in enumerate( $repeat.software_cond.output )
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
179 @CREATE_REPEAT_DIR_1@
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
180 #if str($repeat2.type) == "data"
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
181 #for $k, $file in enumerate($repeat2.input)
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
182 #set file_dir = os.path.join($repeat_dir, 'file_' + str($k))
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
183 #set file_path = os.path.join($file_dir, 'fastqc_data.txt')
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
184 mkdir '$file_dir' &&
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
185 ln -s '$file' '$file_path' &&
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
186 #end for
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
187 #elif str($repeat2.type) == "theoretical_gc"
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
188 #for $file in $repeat2.input
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
189 @ESCAPE_IDENTIFIER@
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
190 #set file_path = os.path.join($repeat_dir, str($identifier) + '_fastqc_theoretical_gc')
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
191 ln -s '$file' '$file_path' &&
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
192 #end for
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
193 #end if
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
194 #end for
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
195 ]]></token>
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
196
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
197 <token name="@RSEQ_INPUT@"><![CDATA[
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
198 #for $j, $repeat2 in enumerate( $repeat.software_cond.output )
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
199 @CREATE_REPEAT_DIR_2@
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
200 #if str($repeat2.type.type) == "bam_stat"
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
201 #set $pattern = "Proper-paired reads map to different chrom:"
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
202 @LN_3_FILES@
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
203 #elif str($repeat2.type.type) == "gene_body_coverage"
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
204 #for $k, $file in enumerate($repeat2.type.input)
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
205 #set file_path = os.path.join($repeat_dir, 'file_' + str($k) + '.geneBodyCoverage.txt')
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
206 ln -s '$file' '$file_path' &&
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
207 #end for
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
208 #elif str($repeat2.type.type) == "inner_distance"
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
209 #for $k, $file in enumerate($repeat2.type.input)
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
210 #set file_path = os.path.join($repeat_dir, 'file_' + str($k) + '.inner_distance_freq.txt')
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
211 ln -s '${file}' '$file_path' &&
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
212 #end for
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
213 #elif str($repeat2.type.type) == "junction_annotation"
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
214 #set $pattern = "Partial Novel Splicing Junctions:"
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
215 @LN_3_FILES@
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
216 #elif str($repeat2.type.type) == "read_gc"
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
217 #for $k, $file in enumerate($repeat2.type.input)
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
218 #set file_path = os.path.join($repeat_dir, 'file_' + str($k) + '.GC.xls')
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
219 ln -s '$file' '$file_path' &&
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
220 #end for
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
221 #elif str($repeat2.type.type) == "junction_annotation"
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
222 #set $pattern = "Group Total_bases Tag_count Tags/Kb"
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
223 @LN_3_FILES@
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
224 #elif str($repeat2.type.type) == "read_distribution"
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
225 #set $pattern = "Group Total_bases Tag_count Tags/Kb"
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
226 @LN_3_FILES@
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
227 #elif str($repeat2.type.type) == "read_duplication_pos"
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
228 #for $k, $file in enumerate($repeat2.type.input)
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
229 #set file_path = os.path.join($repeat_dir, 'file_' + str($k) + '.pos.DupRate.xls')
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
230 ln -s '$file' '$file_path' &&
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
231 #end for
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
232 #elif str($repeat2.type.type) == "infer_experiment"
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
233 #set $pattern = "Fraction of reads explained by"
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
234 #for $file in $repeat2.type.input
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
235 @ESCAPE_IDENTIFIER@
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
236 #set file_path = os.path.join($repeat_dir, str($identifier))
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
237 grep -q "$pattern" $file || die "'$pattern' not found in the file" &&
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
238 ln -s '$file' '$file_path' &&
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
239 #end for
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
240 #end if
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
241 #end for
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
242 ]]></token>
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
243
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
244 <token name="@VCFTOOLS_INPUT@"><![CDATA[
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
245 #for $j, $repeat2 in enumerate( $repeat.software_cond.output )
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
246 @CREATE_REPEAT_DIR_2@
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
247 #if str($repeat2.type.type) == "relatedness2"
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
248 #for $file in $repeat2.type.input
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
249 @ESCAPE_IDENTIFIER@
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
250 #set file_path = os.path.join($repeat_dir, str($identifier) + '.relatedness2')
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
251 ln -s '$file' '$file_path' &&
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
252 #end for
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
253 #elif str($repeat2.type) == "tstv_by_count"
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
254 #for $file in $repeat2.type.input
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
255 @ESCAPE_IDENTIFIER@
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
256 #set file_path = os.path.join($repeat_dir, str($identifier) + '.TsTv.count')
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
257 ln -s '$file' '$file_path' &&
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
258 #end for
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
259 #elif str($repeat2.type) == "tstv_by_qual"
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
260 #for $file in $repeat2.type.input
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
261 @ESCAPE_IDENTIFIER@
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
262 #set file_path = os.path.join($repeat_dir, str($identifier) + '.TsTv.qual')
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
263 ln -s '$file' '$file_path' &&
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
264 #end for
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
265 #elif str($repeat2.type) == "tstv_summary"
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
266 #for $file in $repeat2.type.input
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
267 @ESCAPE_IDENTIFIER@
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
268 #set file_path = os.path.join($repeat_dir, str($identifier) + '.TsTv.summary')
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
269 ln -s '$file' '$file_path' &&
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
270 #end for
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
271 #end if
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
272 #end for
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
273 ]]></token>
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
274
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
275 <token name="@QUALIMAP_INPUT@"><![CDATA[
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
276 #for $file in $repeat.software_cond.input
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
277 #if re.search("genome_results", str($file.element_identifier))
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
278 sample="\$(grep 'bam file = ' $file | sed 's/bam file = //g' | sed 's: ::g')" &&
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
279 dir_name="$software_dir/\${sample}" &&
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
280 mkdir -p \${dir_name} &&
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
281 filepath_1="\${dir_name}/genome_results.txt" &&
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
282 ln -sf '$file' \${filepath_1} &&
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
283 #elif re.search("coverage_histogram", str($file.element_identifier))
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
284 nested_dir_name="\${dir_name}/raw_data_qualimapReport/" &&
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
285 mkdir -p \${nested_dir_name} &&
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
286 filepath_2="\${nested_dir_name}/coverage_histogram.txt" &&
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
287 ln -sf '$file' \${filepath_2} &&
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
288 #elif re.search("gc-content_distribution", str($file.element_identifier))
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
289 nested_dir_name="\${dir_name}/raw_data_qualimapReport/" &&
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
290 mkdir -p \${nested_dir_name} &&
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
291 filepath_3="\${nested_dir_name}/mapped_reads_gc-content_distribution.txt" &&
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
292 ln -sf '$file' \${filepath_3} &&
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
293 #else
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
294 #pass
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
295 #end if
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
296 #end for
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
297 ]]></token>
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
298
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
299 <token name="@SALMON_INPUT@"><![CDATA[
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
300 #for $j, $repeat2 in enumerate( $repeat.software_cond.output )
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
301 @CREATE_REPEAT_DIR_2@
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
302 #if str($repeat2.type.type) == "meta"
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
303 #for $k, $file in enumerate($repeat2.type.input)
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
304 #set file_dir = os.path.join($repeat_dir, 'file_' + str($k))
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
305 #set file_path = os.path.join($file_dir, 'meta_info.json')
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
306 mkdir '$file_dir' &&
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
307 ln -s '$file' '$file_path' &&
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
308 #end for
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
309 #elif str($repeat2.type.type) == "fld"
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
310 #for $k, $file in enumerate($repeat2.type.input)
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
311 #set file_dir = os.path.join($repeat_dir, 'file_' + str($k))
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
312 #set file_path = os.path.join($file_dir,'flenDist.txt')
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
313 mkdir '$file_dir' &&
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
314 ln -s '$file' '$file_path' &&
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
315 #end for
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
316 #end if
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
317 #end for
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
318 ]]></token>
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
319
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
320 <token name="@SAMTOOLS_INPUT@"><![CDATA[
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
321 #for $j, $repeat2 in enumerate( $repeat.software_cond.output )
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
322 @CREATE_REPEAT_DIR_2@
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
323 #if str($repeat2.type.type) == "stats"
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
324 #set $pattern = "This file was produced by samtools stats"
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
325 @LN_3_FILES@
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
326 #elif str($repeat2.type.type) == "flagstat"
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
327 #set $pattern = "in total (QC-passed reads + QC-failed reads)"
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
328 @LN_3_FILES@
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
329 #elif str($repeat2.type.type) == "idxstats"
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
330 #for $file in $repeat2.type.input
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
331 @ESCAPE_IDENTIFIER@
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
332 #set file_path = os.path.join($repeat_dir, str($identifier) + '_idxstat')
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
333 ln -s '$file' '$file_path' &&
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
334 #end for
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
335 #elif str($repeat2.type.type) == "rmdup"
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
336 #set $pattern = "[bam_rmdup"
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
337 @LN_3_FILES@
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
338 #end if
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
339 #end for
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
340 ]]></token>
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
341
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
342 <token name="@STAR_INPUT@"><![CDATA[
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
343 #for $j, $repeat2 in enumerate( $repeat.software_cond.output )
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
344 @CREATE_REPEAT_DIR_2@
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
345 #if str($repeat2.type.type) == "log"
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
346 #for $file in $repeat2.type.input
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
347 @ESCAPE_IDENTIFIER@
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
348 #set file_path = os.path.join($repeat_dir, str($identifier) + '_Log.final.out')
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
iuc
parents:
diff changeset
349 ln -s '$file' '$file_path' &&
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
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350 #end for
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
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351 #elif str($repeat2.type.type) == "genecounts"
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
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352 #for $file in $repeat2.type.input
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
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353 @ESCAPE_IDENTIFIER@
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
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354 #set file_path = os.path.join($repeat_dir, str($identifier) + '_ReadsPerGene.out.tab')
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
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355 ln -s '$file' '$file_path' &&
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
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356 #end for
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
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357 #end if
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
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358 #end for
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
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359 ]]></token>
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
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360
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
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361 <xml name="element_assert" token_name="" token_lines="" token_columns="" token_text="">
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
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362 <element name="@NAME@">
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
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363 <assert_contents>
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
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364 <has_n_columns n="@COLUMNS@"/>
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
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365 <has_n_lines n="@LINES@"/>
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
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366 <has_text text="@TEXT@"/>
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
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367 <yield/>
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
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368 </assert_contents>
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
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369 </element>
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
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370 </xml>
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
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371
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
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372 <xml name="citations">
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
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373 <citations>
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
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374 <citation type="doi">10.1101/gr.244293.118</citation>
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
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375 </citations>
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
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376 </xml>
9a913cdee30e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
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377 </macros>